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- PDB-9xfv: Pilus-like-alpha, a bacteria pilus-like structure obtained from a... -

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Basic information

Entry
Database: PDB / ID: 9xfv
TitlePilus-like-alpha, a bacteria pilus-like structure obtained from a Karst cave from Guilin City, Guangxi Zhuang Autonomous Region, China
Componentsbacteria pilus (like)
KeywordsPROTEIN FIBRIL / Bacteria Pilus
Biological speciesunidentified (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsHu, M.X. / Zhang, Q. / Chen, S. / Ge, Q.J. / Wang, J.W. / Yan, N. / Qin, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190, 92478205 China
CitationJournal: To Be Published
Title: Absolute hand determination of glycofibrils from natural sources in cryo-EM
Authors: Zhang, Q. / Qin, L.J. / Wang, T.T. / Li, Z.Q. / Zhang, Y.L. / Chen, S. / Ge, Q.J. / Yan, N. / Wang, J.W. / Hu, M.X.
History
DepositionOct 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bacteria pilus (like)
B: bacteria pilus (like)
C: bacteria pilus (like)
D: bacteria pilus (like)
E: bacteria pilus (like)
F: bacteria pilus (like)
G: bacteria pilus (like)
H: bacteria pilus (like)
I: bacteria pilus (like)
J: bacteria pilus (like)
K: bacteria pilus (like)
L: bacteria pilus (like)
M: bacteria pilus (like)
N: bacteria pilus (like)
O: bacteria pilus (like)
P: bacteria pilus (like)
Q: bacteria pilus (like)
R: bacteria pilus (like)
S: bacteria pilus (like)
T: bacteria pilus (like)
U: bacteria pilus (like)
V: bacteria pilus (like)
W: bacteria pilus (like)
X: bacteria pilus (like)
Z: bacteria pilus (like)


Theoretical massNumber of molelcules
Total (without water)438,43825
Polymers438,43825
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
bacteria pilus (like)


Mass: 17537.523 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) unidentified (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: dropping water from a Karst cave from Guilin City, Guangxi Province, China
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -76.14 ° / Axial rise/subunit: 11.7 Å / Axial symmetry: C1
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46644 / Symmetry type: HELICAL
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633858
ELECTRON MICROSCOPYf_angle_d0.55645954
ELECTRON MICROSCOPYf_dihedral_angle_d5.514752
ELECTRON MICROSCOPYf_chiral_restr0.0465373
ELECTRON MICROSCOPYf_plane_restr0.0035967

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